libpappsomspp
Library for mass spectrometry
timsframe.h
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1 /**
2  * \file pappsomspp/vendors/tims/timsframe.h
3  * \date 23/08/2019
4  * \author Olivier Langella
5  * \brief handle a single Bruker's TimsTof frame
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  ******************************************************************************/
27 
28 #pragma once
29 
30 #include <memory>
31 #include <QByteArray>
32 #include <vector>
33 #include "../../massspectrum/qualifiedmassspectrum.h"
34 #include "timsframebase.h"
35 #include "../../xic/xic.h"
36 #include "../../msrun/xiccoord/xiccoordtims.h"
37 
38 namespace pappso
39 {
40 
41 class TimsFrame;
42 typedef std::shared_ptr<TimsFrame> TimsFrameSPtr;
43 typedef std::shared_ptr<const TimsFrame> TimsFrameCstSPtr;
44 
45 class TimsBinDec;
46 
48 
49 /**
50  * @todo write docs
51  */
52 class TimsFrame : public TimsFrameBase
53 {
55 
56  public:
57  /**
58  * @param timsId tims frame id
59  * @param scanNum total number of scans in this frame
60  * @param p_bytes pointer on the decompressed binary buffer
61  * @param len size of the decompressed binary buffer
62  */
63  TimsFrame(std::size_t timsId,
64  quint32 scanNum,
65  char *p_bytes,
66  std::size_t len);
67  /**
68  * Copy constructor
69  *
70  * @param other TODO
71  */
72  TimsFrame(const TimsFrame &other);
73 
74  /**
75  * Destructor
76  */
77  virtual ~TimsFrame();
78 
79 
80  virtual std::size_t getNbrPeaks(std::size_t scanNum) const override;
81 
82  /** @brief cumulate scan list into a trace
83  * @param scanNumBegin first scan to cumulate
84  * @param scanNumEnd last scan to cumulate
85  * @return Trace mz and intensity values
86  */
87  virtual Trace cumulateScanToTrace(std::size_t scanNumBegin,
88  std::size_t scanNumEnd) const override;
89 
90  /** @brief cumulate scan list into a trace into a raw spectrum map
91  * @param rawSpectrum simple map of integers to cumulate raw counts
92  * @param scanNumBegin first scan to cumulate
93  * @param scanNumEnd last scan to cumulate
94  */
95  virtual void cumulateScansInRawMap(std::map<quint32, quint32> &rawSpectrum,
96  std::size_t scanNumBegin,
97  std::size_t scanNumEnd) const override;
98 
99 
100  /** @brief get raw index list for one given scan
101  * index are not TOF nor m/z, just index on digitizer
102  */
103  virtual std::vector<quint32> getScanIndexList(std::size_t scanNum) const;
104 
105  /** @brief get raw intensities without transformation from one scan
106  * it needs intensity normalization
107  */
108  virtual std::vector<quint32> getScanIntensities(std::size_t scanNum) const;
109 
110  /** @brief get the mass spectrum corresponding to a scan number
111  * @param scanNum the scan number to retrieve
112  * */
114  getMassSpectrumCstSPtr(std::size_t scanNum) const;
115 
117  getMassSpectrumSPtr(std::size_t scanNum) const override;
118 
119 
120  protected:
121  /** @brief constructor for binary independant tims frame
122  * @param timsId tims frame identifier in the database
123  * @param scanNum the total number of scans contained in this frame
124  */
125  TimsFrame(std::size_t timsId, quint32 scanNum);
126 
128  std::vector<XicCoordTims *>::iterator &itXicListbegin,
129  std::vector<XicCoordTims *>::iterator &itXicListend,
130  XicExtractMethod method) const;
131 
132 
133  /** @brief cumulate a scan into a map
134  *
135  * @param scanNum scan number 0 to (m_scanNumber-1)
136  */
137  virtual void cumulateScan(std::size_t scanNum,
138  std::map<quint32, quint32> &accumulate_into) const;
139 
140 
141  /** @brief get the raw index tof_index and intensities (normalized)
142  *
143  * @param scanNum the scan number to extract
144  * @return trace vector
145  *
146  */
147  virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const;
148 
149 
150  private:
151  /** @brief unshuffle data packet of tims compression type 2
152  * @param src is a zstd decompressed buffer pointer
153  */
154  void unshufflePacket(const char *src);
155 
156 
157  /** @brief get offset for this spectrum in the binary file
158  *
159  * @param scanNum scan number in the frame in the order it lies in binary
160  * file, from 0 to N-1
161  */
162 
163  std::size_t getScanOffset(std::size_t scanNum) const;
164 
165  private:
167  {
168  XicComputeStructure(const TimsFrame *fram_p,
169  const XicCoordTims &xic_struct);
170 
171 
172  Xic *xic_ptr = nullptr;
173  std::size_t mobilityIndexBegin;
174  std::size_t mobilityIndexEnd;
175  std::size_t mzIndexLowerBound;
176  std::size_t mzIndexUpperBound;
177  double tmpIntensity = 0;
178  };
179 
180  protected:
181  QByteArray m_timsDataFrame;
182 };
183 } // namespace pappso
QByteArray m_timsDataFrame
Definition: timsframe.h:181
virtual std::size_t getNbrPeaks(std::size_t scanNum) const override
get the number of peaks in this spectrum need the binary file
Definition: timsframe.cpp:131
virtual ~TimsFrame()
Definition: timsframe.cpp:98
virtual void cumulateScan(std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const
cumulate a scan into a map
Definition: timsframe.cpp:222
TimsFrame(std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
Definition: timsframe.cpp:63
friend TimsDirectXicExtractor
Definition: timsframe.h:54
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override
get Mass spectrum with peaks for this scan number need the binary file
Definition: timsframe.cpp:359
void unshufflePacket(const char *src)
unshuffle data packet of tims compression type 2
Definition: timsframe.cpp:104
std::size_t getScanOffset(std::size_t scanNum) const
get offset for this spectrum in the binary file
Definition: timsframe.cpp:161
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace into a raw spectrum map
Definition: timsframe.cpp:316
virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace
Definition: timsframe.cpp:260
virtual std::vector< quint32 > getScanIndexList(std::size_t scanNum) const
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
Definition: timsframe.cpp:173
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
Definition: timsframe.cpp:198
void extractTimsXicListInRtRange(std::vector< XicCoordTims * >::iterator &itXicListbegin, std::vector< XicCoordTims * >::iterator &itXicListend, XicExtractMethod method) const
Definition: timsframe.cpp:412
virtual pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scanNum) const
get the mass spectrum corresponding to a scan number
Definition: timsframe.cpp:352
virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const
get the raw index tof_index and intensities (normalized)
Definition: timsframe.cpp:504
A simple container of DataPoint instances.
Definition: trace.h:148
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< TimsFrame > TimsFrameSPtr
Definition: timsframe.h:41
std::shared_ptr< Trace > TraceSPtr
Definition: trace.h:135
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
XicExtractMethod
Definition: types.h:200
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition: timsframe.h:43
XicComputeStructure(const TimsFrame *fram_p, const XicCoordTims &xic_struct)
Definition: timsframe.cpp:41
coordinates of the XIC to extract and the resulting XIC after extraction
Definition: xiccoordtims.h:51
handle a single Bruker's TimsTof frame without binary data